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Xiao F, Luo L, Liu X, Ljubetič A, Jin N, Jerala R, Hu G. Comparative Simulative Analysis and Design of Single-Chain Self-Assembled Protein Cages. J Phys Chem B 2024; 128:6272-6282. [PMID: 38904939 DOI: 10.1021/acs.jpcb.4c01957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Coiled-coil protein origami (CCPO) is a modular strategy for the de novo design of polypeptide nanostructures. It represents a type of modular design based on pairwise-interacting coiled-coil (CC) units with a single-chain protein programmed to fold into a polyhedral cage. However, the mechanisms underlying the self-assembly of the protein tetrahedron are still not fully understood. In the present study, 18 CCPO cages with three different topologies were modeled in silico. Then, molecular dynamics simulations and CC parameters were calculated to characterize the dynamic properties of protein tetrahedral cages at both the local and global levels. Furthermore, a deformed CC unit was redesigned, and the stability of the new cage was significantly improved.
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Affiliation(s)
- Fei Xiao
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, Department of Bioinformatics, Center for Systems Biology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215213, China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou 215123, China
| | - Longfei Luo
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, Department of Bioinformatics, Center for Systems Biology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215213, China
| | - Xin Liu
- Institute of Blood and Marrow Transplantation, Medical College of Soochow University, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Collaborative Innovation Center of Hematology, National Clinical Research Center for Hematologic Diseases, Soochow University, Suzhou 215123, China
| | - Ajasja Ljubetič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
- EN-FIST Centre of Excellence, SI-1000 Ljubljana, Slovenia
| | - Nengzhi Jin
- Key Laboratory of Advanced Computing of Gansu Province, Gansu Computing Center, Lanzhou 730030, China
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Guang Hu
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, Department of Bioinformatics, Center for Systems Biology, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215213, China
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou 215123, China
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Bhatia D, Wunder C, Johannes L. Self-assembled, Programmable DNA Nanodevices for Biological and Biomedical Applications. Chembiochem 2021; 22:763-778. [PMID: 32961015 DOI: 10.1002/cbic.202000372] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 09/19/2020] [Indexed: 12/28/2022]
Abstract
The broad field of structural DNA nanotechnology has diverged into various areas of applications ranging from computing, photonics, synthetic biology, and biosensing to in-vivo bioimaging and therapeutic delivery, to name but a few. Though the field began to exploit DNA to build various nanoscale architectures, it has now taken a new path to diverge from structural DNA nanotechnology to functional or applied DNA nanotechnology. More recently a third sub-branch has emerged-biologically oriented DNA nanotechnology, which seeks to explore the functionalities of combinatorial DNA devices in various biological systems. In this review, we summarize the key developments in DNA nanotechnology revealing a current trend that merges the functionality of DNA devices with the specificity of biomolecules to access a range of functions in biological systems. This review seeks to provide a perspective on the evolution and biological applications of DNA nanotechnology, where the integration of DNA structures with biomolecules can now uncover phenomena of interest to biologists and biomedical scientists. Finally, we conclude with the challenges, limitations, and perspectives of DNA nanodevices in fundamental and applied research.
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Affiliation(s)
- Dhiraj Bhatia
- Biological Engineering, Indian Institute of Technology Gandhinagar, Palaj, 382330, Gandhinagar, India
| | - Christian Wunder
- Cellular and Chemical Biology Unit, Endocytic Trafficking and Intracellular Delivery Team U1143 INSERM UMR 3666 CNRS, Institut Curie, PSL Research University, 26 rue d'Ulm, 75248, Paris Cedex 05, France
| | - Ludger Johannes
- Cellular and Chemical Biology Unit, Endocytic Trafficking and Intracellular Delivery Team U1143 INSERM UMR 3666 CNRS, Institut Curie, PSL Research University, 26 rue d'Ulm, 75248, Paris Cedex 05, France
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Intrinsic Dynamics Analysis of a DNA Octahedron by Elastic Network Model. Molecules 2017; 22:molecules22010145. [PMID: 28275219 PMCID: PMC6155889 DOI: 10.3390/molecules22010145] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 01/10/2023] Open
Abstract
DNA is a fundamental component of living systems where it plays a crucial role at both functional and structural level. The programmable properties of DNA make it an interesting building block for the construction of nanostructures. However, molecular mechanisms for the arrangement of these well-defined DNA assemblies are not fully understood. In this paper, the intrinsic dynamics of a DNA octahedron has been investigated by using two types of Elastic Network Models (ENMs). The application of ENMs to DNA nanocages include the analysis of the intrinsic flexibilities of DNA double-helices and hinge sites through the calculation of the square fluctuations, as well as the intrinsic collective dynamics in terms of cross-collective map calculation coupled with global motions analysis. The dynamics profiles derived from ENMs have then been evaluated and compared with previous classical molecular dynamics simulation trajectories. The results presented here revealed that ENMs can provide useful insights into the intrinsic dynamics of large DNA nanocages and represent a useful tool in the field of structural DNA nanotechnology.
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Šponer J, Bussi G, Stadlbauer P, Kührová P, Banáš P, Islam B, Haider S, Neidle S, Otyepka M. Folding of guanine quadruplex molecules-funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies. Biochim Biophys Acta Gen Subj 2016; 1861:1246-1263. [PMID: 27979677 DOI: 10.1016/j.bbagen.2016.12.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/04/2016] [Accepted: 12/11/2016] [Indexed: 01/18/2023]
Abstract
BACKGROUND Guanine quadruplexes (GQs) play vital roles in many cellular processes and are of much interest as drug targets. In contrast to the availability of many structural studies, there is still limited knowledge on GQ folding. SCOPE OF REVIEW We review recent molecular dynamics (MD) simulation studies of the folding of GQs, with an emphasis paid to the human telomeric DNA GQ. We explain the basic principles and limitations of all types of MD methods used to study unfolding and folding in a way accessible to non-specialists. We discuss the potential role of G-hairpin, G-triplex and alternative GQ intermediates in the folding process. We argue that, in general, folding of GQs is fundamentally different from funneled folding of small fast-folding proteins, and can be best described by a kinetic partitioning (KP) mechanism. KP is a competition between at least two (but often many) well-separated and structurally different conformational ensembles. MAJOR CONCLUSIONS The KP mechanism is the only plausible way to explain experiments reporting long time-scales of GQ folding and the existence of long-lived sub-states. A significant part of the natural partitioning of the free energy landscape of GQs comes from the ability of the GQ-forming sequences to populate a large number of syn-anti patterns in their G-tracts. The extreme complexity of the KP of GQs typically prevents an appropriate description of the folding landscape using just a few order parameters or collective variables. GENERAL SIGNIFICANCE We reconcile available computational and experimental studies of GQ folding and formulate basic principles characterizing GQ folding landscapes. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic; Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic.
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy
| | - Petr Stadlbauer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic; Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Barira Islam
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Shozeb Haider
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Stephen Neidle
- UCL School of Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic
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Gkionis K, Kruse H, Šponer J. Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes. J Chem Theory Comput 2016; 12:2000-16. [DOI: 10.1021/acs.jctc.5b01025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Konstantinos Gkionis
- Institute of Biophysics,
Academy of Sciences of the Czech Republic, Královopolská 135, 612
65 Brno, Czech Republic
| | - Holger Kruse
- Institute of Biophysics,
Academy of Sciences of the Czech Republic, Královopolská 135, 612
65 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics,
Academy of Sciences of the Czech Republic, Královopolská 135, 612
65 Brno, Czech Republic
- CEITEC
− Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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Iacovelli F, Falconi M, Knudsen BR, Desideri A. Comparative simulative analysis of single and double stranded truncated octahedral DNA nanocages. RSC Adv 2016. [DOI: 10.1039/c5ra27591a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Spacefill view of double (DSL) and single (SSL) stranded linkers DNA cages. The blue atoms represent the shared cages scaffold, while the yellow atoms show the single stranded DNA oligonucleotides shaping the double stranded linkers of the DSL cage.
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Affiliation(s)
| | - Mattia Falconi
- Department of Biology
- University of Rome “Tor Vergata”
- 00133 Rome
- Italy
| | - Birgitta R. Knudsen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics
- Åarhus University
- Åarhus
- Denmark
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Stadlbauer P, Kührová P, Banáš P, Koča J, Bussi G, Trantírek L, Otyepka M, Šponer J. Hairpins participating in folding of human telomeric sequence quadruplexes studied by standard and T-REMD simulations. Nucleic Acids Res 2015; 43:9626-44. [PMID: 26433223 PMCID: PMC4787745 DOI: 10.1093/nar/gkv994] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 09/22/2015] [Indexed: 11/13/2022] Open
Abstract
DNA G-hairpins are potential key structures participating in folding of human telomeric guanine quadruplexes (GQ). We examined their properties by standard MD simulations starting from the folded state and long T-REMD starting from the unfolded state, accumulating ∼130 μs of atomistic simulations. Antiparallel G-hairpins should spontaneously form in all stages of the folding to support lateral and diagonal loops, with sub-μs scale rearrangements between them. We found no clear predisposition for direct folding into specific GQ topologies with specific syn/anti patterns. Our key prediction stemming from the T-REMD is that an ideal unfolded ensemble of the full GQ sequence populates all 4096 syn/anti combinations of its four G-stretches. The simulations can propose idealized folding pathways but we explain that such few-state pathways may be misleading. In the context of the available experimental data, the simulations strongly suggest that the GQ folding could be best understood by the kinetic partitioning mechanism with a set of deep competing minima on the folding landscape, with only a small fraction of molecules directly folding to the native fold. The landscape should further include non-specific collapse processes where the molecules move via diffusion and consecutive random rare transitions, which could, e.g. structure the propeller loops.
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Affiliation(s)
- Petr Stadlbauer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jaroslav Koča
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic National Center for Biomolecular Research, Faculty of Science, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea 265, 34136 Trieste, Italy
| | - Lukáš Trantírek
- CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic CEITEC - Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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